Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field
J Karwounopoulos, Å Kaupang, M Wieder… - Journal of Chemical …, 2023 - ACS Publications
… for the computational prediction of transfer free energies, ie, … charge models together with
the OPLS-AA force field. (34) … tend to be too positive, so the LRC on average improves the …
the OPLS-AA force field. (34) … tend to be too positive, so the LRC on average improves the …
… of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike organic molecules
D Vassetti, M Pagliai, P Procacci - Journal of chemical theory and …, 2019 - ACS Publications
… Also the improvement with respect to GAFF1 (green square in … the OPLS-AA are strongly
affected by the predicted hydration … If we eliminate the outlier dialifor, OPLS-AA MUE improves …
affected by the predicted hydration … If we eliminate the outlier dialifor, OPLS-AA MUE improves …
[HTML][HTML] MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning
… solvation processes and is capable of strengthening various … Color shading depicts the
predicted hydration free energies … to low and high hydration free energy cases, respectively. The …
predicted hydration free energies … to low and high hydration free energy cases, respectively. The …
CHARMM-GUI free energy calculator for absolute and relative ligand solvation and binding free energy simulations
… free energy simulations have long been utilized to predict … of Free Energy Calculator,
which will be improved in the future. … for FEP calculations, using different ligand force fields …
which will be improved in the future. … for FEP calculations, using different ligand force fields …
PyAutoFEP: An automated free energy perturbation workflow for GROMACS integrating enhanced sampling methods
L Carvalho Martins, EA Cino… - Journal of Chemical …, 2021 - ACS Publications
… improved predictions compared to CHARMM36m. Finally, we estimated the probability of
finding a molecule 1 pK i better than a lead when using … RMSEc, our predictions using OPLS-AA…
finding a molecule 1 pK i better than a lead when using … RMSEc, our predictions using OPLS-AA…
Prediction of octanol-water partition coefficients for the SAMPL6- molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force …
… Absolute solvation free energies were computed by … protocol using 5-ns windowed alchemical
free energy perturbation (FEP) … improved the RMSE of the GAFF \(\log P_{ow}\) predictions …
free energy perturbation (FEP) … improved the RMSE of the GAFF \(\log P_{ow}\) predictions …
Using AMBER18 for relative free energy calculations
… could help enhance the overall sampling and improve the … errors above those seen using
the FEP/OPLS 2.1 force field. … the capabilities of the next generation GAFF2 and protein force …
the FEP/OPLS 2.1 force field. … the capabilities of the next generation GAFF2 and protein force …
[HTML][HTML] A fast and high-quality charge model for the next generation general AMBER force field
… excellent performance in the solvation free energy (SFE) … used for the absolute or relative
protein-ligand binding free energy … a feasible way to greatly improve the performance of GAFF2/…
protein-ligand binding free energy … a feasible way to greatly improve the performance of GAFF2/…
Hybrid alchemical free energy/machine-learning methodology for the computation of hydration free energies
… hydration free energies with the OPLS hydration free energies (Pearson r 0.95, mean absolute
… QM derived corrections to improve GAFF hydration free energies reported in submission …
… QM derived corrections to improve GAFF hydration free energies reported in submission …
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules
A Chakravorty, A Hussain, LF Cervantes… - Journal of Chemical …, 2024 - ACS Publications
… with other contemporaneous ones like OPLS. Here, we analyze … the absolute hydration free
energy of over 600 small molecules, … The improved MAE and RMSE values (compared to our …
energy of over 600 small molecules, … The improved MAE and RMSE values (compared to our …